A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
/nfs/home/rsbg/01_fastq/04_emily_ebel_bulk_midgut_data_eg_RNAseq/HunterPipeline/02_Hisat2/logs
General Statistics
| Sample Name | % Aligned |
|---|---|
| 22_WNV_A_S1 | 44.4% |
| 22_WNV_B_S2 | 46.6% |
| 22_WNV_C_S3 | 36.9% |
| 22_mock_A_S4 | 71.5% |
| 22_mock_B_S5 | 41.0% |
| 22_mock_C_S6 | 14.3% |
| 26_WNV_A_S7 | 15.4% |
| 26_WNV_B_S8 | 13.4% |
| 26_WNV_C_S9 | 17.6% |
| 26_mock_A_S10 | 44.7% |
| 26_mock_B_S11 | 41.4% |
| 26_mock_C_S12 | 17.3% |
| 30_WNV_A_S13 | 62.5% |
| 30_WNV_B_S14 | 54.4% |
| 30_WNV_C_S15 | 57.5% |
| 30_mock_A_S16 | 46.7% |
| 30_mock_B_S17 | 70.1% |
| 30_mock_C_S18 | 68.1% |
Bowtie 2 / HiSAT2
Results from both Bowtie 2 and HISAT2, tools for aligning reads against a reference genome.URL: http://bowtie-bio.sourceforge.net/bowtie2; https://ccb.jhu.edu/software/hisat2DOI: 10.1038/nmeth.1923; 10.1038/nmeth.3317; 10.1038/s41587-019-0201-4
Paired-end alignments
This plot shows the number of reads aligning to the reference in different ways.
There are 6 possible types of alignment:
- PE mapped uniquely: Pair has only one occurence in the reference genome.
- PE mapped discordantly uniquely: Pair has only one occurence but not in proper pair.
- PE one mate mapped uniquely: One read of a pair has one occurence.
- PE multimapped: Pair has multiple occurence.
- PE one mate multimapped: One read of a pair has multiple occurence.
- PE neither mate aligned: Pair has no occurence.